Toolbox for the processing and analysis of MALDI-MSI data
Project description
uMAIA
Toolbox for the processing and analysis of MALDI-MSI data
Installation
To begin, install the environment by navigating to the /uMAIA directory and running python3 setup.py
. The command was tested with Python version 3.7.16.
Gurobi
The molecule matching portion of the pipeline requires Gurobi. You will need to (1) install the Gurobi installer and (2) activate a license that is free for those are affiliated with an academic institution. Concerning (1), download the archive with
wget https://packages.gurobi.com/9.1/gurobi9.1.2_linux64.tar.gz
to the directory you want to install it in.
Unpack the archive with
tar -xzvf gurobi9.1.2_linux64.tar.gz
Activate the license with
gurobi912/linux64/bin/grbgetkey <licensekey>
GPU usage restrictions
If you intend on applying uMAIA's normalisation algorithm on a GPU, please note that JAX will automatically use between 75 and 90 % of available GPU memory. To indicate that you would only like to allocate memory that is needed, you may export an environment variable after activating the environment with export XLA_PYTHON_CLIENT_PREALLOCATE=false
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